[2024-01-24 14:19:21,633] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:19:21,645] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:19:21,646] [INFO] DQC Reference Directory: /var/lib/cwl/stg92b59390-6787-4c5f-bc15-5d4e448eb59e/dqc_reference
[2024-01-24 14:19:23,546] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:19:23,549] [INFO] Task started: Prodigal
[2024-01-24 14:19:23,549] [INFO] Running command: gunzip -c /var/lib/cwl/stg3fa4b42f-5e48-479c-9be2-b91f970b0971/GCF_022698165.1_ASM2269816v1_genomic.fna.gz | prodigal -d GCF_022698165.1_ASM2269816v1_genomic.fna/cds.fna -a GCF_022698165.1_ASM2269816v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:19:54,614] [INFO] Task succeeded: Prodigal
[2024-01-24 14:19:54,615] [INFO] Task started: HMMsearch
[2024-01-24 14:19:54,615] [INFO] Running command: hmmsearch --tblout GCF_022698165.1_ASM2269816v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg92b59390-6787-4c5f-bc15-5d4e448eb59e/dqc_reference/reference_markers.hmm GCF_022698165.1_ASM2269816v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:19:55,152] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:19:55,153] [INFO] Found 6/6 markers.
[2024-01-24 14:19:55,256] [INFO] Query marker FASTA was written to GCF_022698165.1_ASM2269816v1_genomic.fna/markers.fasta
[2024-01-24 14:19:55,256] [INFO] Task started: Blastn
[2024-01-24 14:19:55,256] [INFO] Running command: blastn -query GCF_022698165.1_ASM2269816v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg92b59390-6787-4c5f-bc15-5d4e448eb59e/dqc_reference/reference_markers.fasta -out GCF_022698165.1_ASM2269816v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:19:58,554] [INFO] Task succeeded: Blastn
[2024-01-24 14:19:58,557] [INFO] Selected 27 target genomes.
[2024-01-24 14:19:58,558] [INFO] Target genome list was writen to GCF_022698165.1_ASM2269816v1_genomic.fna/target_genomes.txt
[2024-01-24 14:19:58,574] [INFO] Task started: fastANI
[2024-01-24 14:19:58,574] [INFO] Running command: fastANI --query /var/lib/cwl/stg3fa4b42f-5e48-479c-9be2-b91f970b0971/GCF_022698165.1_ASM2269816v1_genomic.fna.gz --refList GCF_022698165.1_ASM2269816v1_genomic.fna/target_genomes.txt --output GCF_022698165.1_ASM2269816v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:21:08,582] [INFO] Task succeeded: fastANI
[2024-01-24 14:21:08,583] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg92b59390-6787-4c5f-bc15-5d4e448eb59e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:21:08,584] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg92b59390-6787-4c5f-bc15-5d4e448eb59e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:21:08,734] [INFO] Found 27 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:21:08,734] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:21:08,735] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Streptomyces panaciradicis	strain=NBRC 109811	GCA_023516615.1	1470261	1470261	type	True	87.8411	2173	3625	95	below_threshold
Streptomyces plumbidurans	strain=KC 17012	GCA_019857225.1	2814589	2814589	type	True	87.2612	2047	3625	95	below_threshold
Streptomyces justiciae	strain=3R004	GCA_015163075.1	2780140	2780140	type	True	86.6075	2360	3625	95	below_threshold
Streptomyces aquilus	strain=GGCR-6	GCA_003955715.1	2548456	2548456	type	True	86.5952	2315	3625	95	below_threshold
Streptomyces antibioticus	strain=DSM 40234	GCA_001514065.1	1890	1890	suspected-type	True	86.4431	2255	3625	95	below_threshold
Streptomyces pseudovenezuelae	strain=DSM 40212	GCA_001513955.1	67350	67350	type	True	86.2412	2229	3625	95	below_threshold
Streptomyces canus	strain=DSM 40017	GCA_001514145.1	58343	58343	suspected-type	True	85.9988	2301	3625	95	below_threshold
Streptomyces dysideae	strain=RV15	GCA_001514305.1	909626	909626	type	True	85.8813	2090	3625	95	below_threshold
Streptomyces ferrugineus	strain=CCTCC AA2014009	GCA_015160855.1	1413221	1413221	type	True	85.8275	2169	3625	95	below_threshold
Streptomyces caeruleatus	strain=NRRL B-24802	GCA_001514235.1	661399	661399	type	True	85.8261	2161	3625	95	below_threshold
Streptomyces lanatus	strain=JCM 4588	GCA_014655715.1	66900	66900	type	True	85.66	2192	3625	95	below_threshold
Streptomyces davaonensis	strain=JCM 4913	GCA_000349325.1	348043	348043	type	True	85.659	2048	3625	95	below_threshold
Streptomyces cellostaticus	strain=DSM 40189	GCA_001513965.1	67285	67285	type	True	85.3718	2025	3625	95	below_threshold
Streptomyces shenzhenensis subsp. oryzicola	strain=W18L9	GCA_013870495.1	2749088	943815	type	True	85.2953	1562	3625	95	below_threshold
Streptomyces phaeofaciens	strain=JCM 4125	GCA_014648915.1	68254	68254	type	True	85.2414	2098	3625	95	below_threshold
Streptomyces griseoruber	strain=NRRL B-1818	GCA_001418585.1	1943	1943	type	True	85.148	1723	3625	95	below_threshold
Streptomyces chromofuscus	strain=DSM 40273	GCA_015160875.1	42881	42881	type	True	85.093	1763	3625	95	below_threshold
Streptomyces chromofuscus	strain=JCM 4354	GCA_014649435.1	42881	42881	type	True	84.9882	1784	3625	95	below_threshold
Streptomyces shenzhenensis	strain=DSM 42034	GCA_021462265.1	943815	943815	type	True	84.9521	2114	3625	95	below_threshold
Streptomyces rishiriensis	strain=NBRC 13407	GCA_003112535.1	68264	68264	type	True	84.8695	1942	3625	95	below_threshold
Streptomyces galbus	strain=JCM 4639	GCA_014650535.1	33898	33898	type	True	84.8089	1828	3625	95	below_threshold
Streptomyces durhamensis	strain=NRRL B-3309	GCA_000725475.1	68194	68194	type	True	84.7519	1915	3625	95	below_threshold
Streptomyces leeuwenhoekii	strain=C34 (= DSM 42122 = NRRL B-24963)	GCA_001013905.1	1437453	1437453	type	True	84.449	1695	3625	95	below_threshold
Streptomyces brasiliscabiei	strain=IBSBF 2867	GCA_018927715.1	2736302	2736302	type	True	83.969	1903	3625	95	below_threshold
Streptomyces bottropensis	strain=ATCC 25435	GCA_000383595.1	42235	42235	type	True	83.895	1860	3625	95	below_threshold
Streptomyces bottropensis	strain=ATCC 25435	GCA_000340335.2	42235	42235	type	True	83.8082	1854	3625	95	below_threshold
Streptomyces ossamyceticus	strain=NRRL B-3822	GCA_001418475.1	249581	249581	type	True	83.7361	1568	3625	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:21:08,737] [INFO] DFAST Taxonomy check result was written to GCF_022698165.1_ASM2269816v1_genomic.fna/tc_result.tsv
[2024-01-24 14:21:08,737] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:21:08,738] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:21:08,738] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg92b59390-6787-4c5f-bc15-5d4e448eb59e/dqc_reference/checkm_data
[2024-01-24 14:21:08,749] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:21:08,862] [INFO] Task started: CheckM
[2024-01-24 14:21:08,862] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_022698165.1_ASM2269816v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_022698165.1_ASM2269816v1_genomic.fna/checkm_input GCF_022698165.1_ASM2269816v1_genomic.fna/checkm_result
[2024-01-24 14:24:05,127] [INFO] Task succeeded: CheckM
[2024-01-24 14:24:05,129] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:24:05,156] [INFO] ===== Completeness check finished =====
[2024-01-24 14:24:05,156] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:24:05,157] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_022698165.1_ASM2269816v1_genomic.fna/markers.fasta)
[2024-01-24 14:24:05,157] [INFO] Task started: Blastn
[2024-01-24 14:24:05,157] [INFO] Running command: blastn -query GCF_022698165.1_ASM2269816v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg92b59390-6787-4c5f-bc15-5d4e448eb59e/dqc_reference/reference_markers_gtdb.fasta -out GCF_022698165.1_ASM2269816v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:24:09,727] [INFO] Task succeeded: Blastn
[2024-01-24 14:24:09,731] [INFO] Selected 24 target genomes.
[2024-01-24 14:24:09,731] [INFO] Target genome list was writen to GCF_022698165.1_ASM2269816v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:24:09,757] [INFO] Task started: fastANI
[2024-01-24 14:24:09,757] [INFO] Running command: fastANI --query /var/lib/cwl/stg3fa4b42f-5e48-479c-9be2-b91f970b0971/GCF_022698165.1_ASM2269816v1_genomic.fna.gz --refList GCF_022698165.1_ASM2269816v1_genomic.fna/target_genomes_gtdb.txt --output GCF_022698165.1_ASM2269816v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:25:12,284] [INFO] Task succeeded: fastANI
[2024-01-24 14:25:12,363] [INFO] Found 24 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 14:25:12,364] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCF_004343515.1	s__Streptomyces sp004343515	88.0516	2350	3625	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.56	96.56	0.86	0.86	2	-
GCF_000720765.1	s__Streptomyces sp000720765	87.9589	2441	3625	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.07	96.07	0.83	0.83	2	-
GCF_001484565.1	s__Streptomyces sp001484565	87.8444	2303	3625	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006715395.1	s__Streptomyces sp006715395	87.803	2306	3625	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.35	95.35	0.79	0.79	2	-
GCF_003384795.1	s__Streptomyces sp003384795	87.7333	2279	3625	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002754715.1	s__Streptomyces sp002754715	87.6375	2355	3625	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002027195.1	s__Streptomyces sp002027195	86.7327	1897	3625	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0044	N/A	N/A	N/A	N/A	1	-
GCF_003955715.1	s__Streptomyces aquilus	86.5925	2315	3625	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.2614	97.56	95.79	0.89	0.84	3	-
GCF_003143935.1	s__Streptomyces sp003143935	86.523	2257	3625	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000972385.1	s__Streptomyces sp000972385	86.3975	2150	3625	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013044505.1	s__Streptomyces sp013044505	86.3552	2190	3625	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001513955.1	s__Streptomyces pseudovenezuelae	86.2662	2223	3625	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000383615.1	s__Streptomyces canus_C	86.1362	2227	3625	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0589	N/A	N/A	N/A	N/A	1	-
GCF_001514145.1	s__Streptomyces canus	85.9818	2304	3625	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.82	96.31	0.85	0.84	3	-
GCF_001746295.1	s__Streptomyces sp001746295	85.928	2299	3625	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000720805.1	s__Streptomyces violaceoruber_B	85.8001	2049	3625	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	96.8346	N/A	N/A	N/A	N/A	1	-
GCF_014257025.1	s__Streptomyces sp014257025	85.7954	1973	3625	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000349325.1	s__Streptomyces davaonensis	85.6692	2045	3625	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004346005.1	s__Streptomyces sp004346005	85.4677	2062	3625	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003814875.1	s__Streptomyces sp003814875	85.3784	2233	3625	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015160875.1	s__Streptomyces chromofuscus	85.0918	1764	3625	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.96	99.96	0.98	0.98	2	-
GCF_001514285.1	s__Streptomyces sp001514285	85.0221	1953	3625	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000317595.1	s__Streptomyces ipomoeae	83.9264	1785	3625	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.29	98.81	0.89	0.87	4	-
GCF_001418475.1	s__Streptomyces ossamyceticus	83.7734	1562	3625	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.6547	98.97	98.97	0.90	0.90	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:25:12,366] [INFO] GTDB search result was written to GCF_022698165.1_ASM2269816v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:25:12,370] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:25:12,378] [INFO] DFAST_QC result json was written to GCF_022698165.1_ASM2269816v1_genomic.fna/dqc_result.json
[2024-01-24 14:25:12,378] [INFO] DFAST_QC completed!
[2024-01-24 14:25:12,378] [INFO] Total running time: 0h5m51s